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- EMDB-10706: Cryo-EM structure of a Phenuiviridae L protein -

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Basic information

Entry
Database: EMDB / ID: EMD-10706
TitleCryo-EM structure of a Phenuiviridae L protein
Map data
Sample
  • Complex: Severe Fever with Thrombocytopenia Syndrome Virus L Protein
    • Protein or peptide: RNA-dependent RNA polymerase
  • Ligand: MAGNESIUM ION
KeywordsBunyavirus / Phenuiviridae / L protein / viral polymerase / cap-snatching / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesSFTS virus AH12
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsVogel D / Thorkelsson SR
Funding support Germany, 2 items
OrganizationGrant numberCountry
Leibniz AssociationK27/2017 Germany
German Research Foundation (DFG)INST 152/777-1 FUGG Germany
CitationJournal: J Struct Biol / Year: 2012
Title: RELION: implementation of a Bayesian approach to cryo-EM structure determination.
Authors: Sjors H W Scheres /
Abstract: RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) ...RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs.
History
DepositionFeb 26, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseApr 8, 2020-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6y6k
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10706.png

Downloads & links

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Map

FileDownload / File: emd_10706.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.87 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.20976333 - 0.35944355
Average (Standard dev.)0.0008863566 (±0.013343462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 174.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z174.000174.000174.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2100.3590.001

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Supplemental data

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Sample components

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Entire : Severe Fever with Thrombocytopenia Syndrome Virus L Protein

EntireName: Severe Fever with Thrombocytopenia Syndrome Virus L Protein
Components
  • Complex: Severe Fever with Thrombocytopenia Syndrome Virus L Protein
    • Protein or peptide: RNA-dependent RNA polymerase
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Severe Fever with Thrombocytopenia Syndrome Virus L Protein

SupramoleculeName: Severe Fever with Thrombocytopenia Syndrome Virus L Protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: SFTS virus AH12
Molecular weightTheoretical: 238 KDa

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Macromolecule #1: RNA-dependent RNA polymerase

MacromoleculeName: RNA-dependent RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: SFTS virus AH12
Molecular weightTheoretical: 235.742531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLEVLCGRI NVENGLSLGE PGLYDQIYDR PGLPDLDVTV DATGVTVDIG AVPDSASQLG SSINAGLITI QLSEAYKINH DFTFSGLSK TTDRRLSEVF PITHDGSDGM TPDVIHTRLD GTIVVVEFST TRSHNIGGLE AAYRTKIEKY RDPISRRVDI M ENPRVFFG ...String:
MNLEVLCGRI NVENGLSLGE PGLYDQIYDR PGLPDLDVTV DATGVTVDIG AVPDSASQLG SSINAGLITI QLSEAYKINH DFTFSGLSK TTDRRLSEVF PITHDGSDGM TPDVIHTRLD GTIVVVEFST TRSHNIGGLE AAYRTKIEKY RDPISRRVDI M ENPRVFFG VIVVSSGGVL SNMPLTQDEA EELMYRFCIA NEIYTKARSM DADIELQKSE EELEAISRAL SFFSLFEPNI ER VEGTFPN SEIKMLEQFL STPADVDFIT KTLKAKEVEA YADLCDSHYL KPEKTIQERL EINRCEAIDK TQDLLAGLHA RSN KQTSLN RGTVKLPPWL PKPSSESIDI KTDSGFGSLM DHGAYGELWA KCLLDVSLGN VEGVVSDPAK ELDIAISDDP EKDT PKEAK ITYRRFKPAL SSSARQEFSL QGVEGKKWKR MAANQKKEKE SHETLSPFLD VEDIGDFLTF NNLLTDSRYG DESIQ RAVS ILLEKASAMQ DTELTHALND SFKRNLSSNV VQWSLWVSCL AQELASALKQ HCRAGEFIIK KLKFWPIYVI IKPTKS SSH IFYSLGIRKA DVTRRLTGRV FSDTIDAGEW ELTEFKSLKT CKLTNLVNLP CTMLNSIAFW REKLGVAPWL VRKPCSE LR EQVGLTFLIS LEDKSKTEEI ITLTRYTQME GFVSPPMLPK PQKMLGKLDG PLRTKLQVYL LRKHLDCMVR IASQPFSL I PREGRVEWGG TFHAISGRST NLENMVNSWY IGYYKNKEES TELNALGEMY KKIVEMEEDK PSSPEFLGWG DTDSPKKHE FSRSFLRAAC SSLEREIAQR HGRQWKQNLE ERVLREIGTK NILDLASMKA TSNFSKDWEL YSEVQTKEYH RSKLLEKMAT LIEKGVMWY IDAVGQAWKA VLDDGCMRIC LFKKNQHGGL REIYVMDANA RLVQFGVETM ARCVCELSPH ETVANPRLKN S IIENHGLK SARSLGPGSI NINSSNDAKK WNQGHYTTKL ALVLCWFMPA KFHRFIWAAI SMFRRKKMMV DLRFLAHLSS KS ESRSSDP FREAMTDAFH GNRDVSWMDK GRTYIKTETG MMQGILHFTS SLLHSCVQSF YKSYFVSKLK EGYMGESISG VVD VIEGSD DSAIMISIRP KSDMDEVRSR FFVANLLHSV KFLNPLFGIY SSEKSTVNTV YCVEYNSEFH FHRHLVRPTL RWIA ASHQI SETEALASRQ EDYSNLLTQC LEGGASFSLT YLIQCAQLLH HYMLLGLCLH PLFGTFMGML ISDPDPALGF FLMDN PAFA GGAGFRFNLW RACKTTDLGR KYAYYFNEIQ GKTKGDEDYR ALDATSGGTL SHSVMVYWGD RKKYQALLNR MGLPED WVE QIDENPGVLY RRAANKKELL LKLAEKVHSP GVTSSLSKGH VVPRVVAAGV YLLSRHCFRF SSSIHGRGST QKASLIK LL MMSSISAMKH GGSLNPNQER MLFPQAQEYD RVCTLLEEVE HLTGKFVVRE RNIVRSRIDL FQEPVDLRCK AEDLVSEV W FGLKRTKLGP RLLKEEWDKL RASFAWLSTD PSETLRDGPF LSHVQFRNFI AHVDAKSRSV RLLGAPVKKS GGVTTISQV VRMNFFPGFS LEAEKSLDNQ ERLESISILK HVLFMVLNGP YTEEYKLEMI IEAFSTLVIP QPSEVIRKSR TMTLCLLSNY LSSRGGSIL DQIERAQSGT LGGFSKPQKT FVRPGGGVGY KGKGVWTGVM EDTHVQILID GDGTSNWLEE IRLSSDARLY D VIESIRRL CDDLGINNRV ASAYRGHCMV RLSGFKIKPA SRTDGCPVRI MERGFRIREL QNPDEVKMRV RGDILNLSVT IQ EGRVMNI LSYRPRDTDI SESAAAYLWS NRDLFSFGKK EPSCSWICLK TLDNWAWSHA SVLLANDRKT QGIDNRAMGN IFR DCLEGS LRKQGLMRSK LTEMVEKNVV PLTTQELVDI LEEDIDFSDV IAVELSEGSL DIESIFDGAP ILWSAEVEEF GEGV VAVSY SSKYYHLTLM DQAAITMCAI MGKEGCRGLL TEKRCMAAIR EQVRPFLIFL QIPEDSISWV SDQFCDSRGL DEEST IMWG

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.15 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
500.0 mMNaClSodium chloridesodium chloride
20.0 mMMgClmagnesium chloride
GridModel: Quantifoil R2/1 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Details: Harrick Plasma cleaner
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2s using blotting force -10.

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2626 / Average exposure time: 3.0 sec. / Average electron dose: 59.45 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 780000
Details: Particles were picked with Warp's pretrained agent BoxNet2Mask_20180918
Startup modelType of model: OTHER
Details: An ab initio model generated by cisTEM from a screening dataset.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 220000

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 225.217
Output model

PDB-6y6k:
Cryo-EM structure of a Phenuiviridae L protein

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